Role of N6-methyladenosine methylation in nasopharyngeal carcinoma: current insights and future prospective

Abstract

Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck squamous cell carcinoma prevalent in Southern China, Southeast Asia, and North Africa. Despite advances in treatment options, the prognosis for advanced NPC remains poor, underscoring the urgent need to explore its underlying mechanisms and develop novel therapeutic strategies. Epigenetic alterations have been shown to play a key role in NPC progression. Recent studies indicate that dysregulation of RNA modifications in NPC specifically affects tumor-related transcripts, influencing various oncogenic processes. This review provides a comprehensive overview of altered RNA modifications and their regulators in NPC, with a focus on m⁶A and its regulatory mechanisms. We discuss how m⁶A RNA modification influences gene expression and affects NPC initiation and progression at the molecular level, analyzing its impact on cancer-related biological functions. Understanding these modifications could reveal new biomarkers and therapeutic targets for NPC, offering promising directions for future research and precision medicine.

Fig. 1. Expression and oncogenic roles of RNA modification regulators in NPC.

A m⁶A RNA modification: The methyltransferase complex (MTC), composed of METTL3, METTL14, WTAP, VIRMA, and additional subunits, primarily catalyzes m⁶A modifications on RNA. Two demethylases, FTO and ALKBH5, remove m⁶A marks from modified RNAs. Additional m⁶A methyltransferases, such as the METTL5-TRIM112 complex and ZCCHC4, specifically add m⁶A modifications to 18S and 28S rRNAs, respectively. Reader proteins recognize m⁶A sites, including YTH domain-containing proteins (YTHDF1/2/3, YTHDC1/2), IGF2BP1/2/3, and HNRNPs. B m⁵C RNA modification: m⁵C methylation is catalyzed by RNA-type-specific NSUN family proteins and NOP2, while TET family enzymes remove m⁵C marks. Reader proteins YBX1 and ALYREF recognize m⁵C modifications. C m⁷G RNA modification: The METTL1-WDR4 complex installs m⁷G modifications on mRNAs and tRNAs. Oncogenic proteins in NPC are highlighted in red, tumor suppressors in green, and proteins with undefined roles in gray. Upward arrows indicate proteins upregulated in NPC, while downward arrows denote downregulated proteins.

Fig. 2. Roles of m⁶A modifications in gene regulation.

A RNA stability and decay. (1) YTHDF2 promotes decay of m⁶A-modified RNA by recruiting: (1) the CCR4-NOT complex for deadenylation, (2) RNaseP/MRP endonucleases for cleavage, and (3) UPF1/PNRC2/DCP1A for decapping. YTHDF1 facilitates EBV transcripts degradation. YTHDF3 interacts with YTHDF2 to support mRNA decay. (4) YTHDC1 stabilizes splicing factor mRNAs by inhibiting NMD via m⁶A. (5) YTHDC2 promotes mRNA decay through XRN1-mediated exoribonucleolytic cleavage. (6) The IGF2BP family stabilizes mRNAs by recruiting HuR, MATR3, and PABPC1, forming protective ribonucleoprotein granules under stress. B RNA translation. (1) YTHDF1 promotes cap-dependent translation by connecting m⁶A-modified mRNAs to ribosomes, coordinated by YTHDF3. METTL3 supports translation initiation via eIF3h, facilitating mRNA circularization. (2) eIF3 also enables cap-independent translation by targeting m⁶A in the 5′-UTR. Under stress, YTHDF2 maintains 5′ UTR methylation for selective mRNA translation. (3) YTHDC2 aids translation elongation by resolving m⁶A-modified structures. (4) IGF2BPs enhance translation by forming ribonucleoprotein granules. C RNA processing and export. (1) YTHDC1 regulates splicing by recruiting SRSF2/3 for exon inclusion or SRSF10 for exon skipping, with HNRNPA2B1 also influencing splicing. HNRNPA2B1/m⁶A aids miRNA formation by directing the DGCR8-DROSHA complex to pri-miRNAs. (2) YTHDC1 facilitates the export of m⁶A-modified mRNAs to the cytoplasm through SRSF3 and NXF1, while also directing the export of circRNAs, such as circNSUN2. (3) YTHDC1 recruits DDX5 to assist in the backsplicing required for circRNA formation. (4) YTHDF3 and eIF4G2 regulate circ-ZNF609 translation. (5) METTL16 supports SAM levels by promoting splicing of retained introns in MAT2A. D Transcriptional regulation. (1) m⁶A modifications are critical for regulating transcription by controlling TF expression. (2) m⁶A influences RNAP II pausing at promoters by recruiting MTC and YTHDC1, facilitating RNAP II release. (3) m⁶A marks on eRNAs attract YTHDC1 to form condensates crucial for BRD4 activation. (4) MTC-deposited m⁶A modifications at promoters and enhancers prevent early integrator-mediated termination, ensuring robust transcription. E Histone modifications. (1) METTL14-mediated m⁶A destabilizes transcripts for histone modifiers, influencing histone marks such as H3K27me3, H3K27ac, and H3K4me3 in neural stem cells. (2) YTHDC1 recruits KDM3B to demethylate H3K9me2, promoting gene expression. (3) H3K36me3, mediated by SETD2, attracts METTL14 to facilitate global m⁶A deposition on actively transcribed RNAs. F Chromatin integrity. (1) METTL3 and YTHDC1, along with SETDB1 and TRIM28, uphold heterochromatin integrity by silencing retrotransposons. (2) m⁶A stabilizes chromatin by promoting MSR transcript association. (3) YTHDC1-mediated destabilization of methylated carRNAs regulates local chromatin states. (4) In R-loops, m⁶A recognized by YTHDF2 prevents R-loop accumulation, which can lead to genomic instability and R-loop-dependent DSBs. (5) At DSB sites, ATM-mediated phosphorylation of METTL3 recruits YTHDC1 to safeguard RNA-DNA hybrids, facilitating RAD51, BRCA1, and RNAP II-mediated homologous recombination repair. (6) DDX21 anchors METTL3 for m⁶A deposition at transcription termination sites, recruiting XRN2 to ensure transcription termination and maintain genomic stability.

Fig. 3. Roles of RNA Modifications in Oncogenic Signaling Pathways, EMT, and Cancer Stemness in NPC.

A Oncogenic Signaling Pathways: (1) m⁶A modification of TEAD4 mRNA, recognized by YTHDF2, stabilizes TEAD4, leading to its upregulation, which promotes BZW2 transcription and inhibits PHLPP2, thus activating the AKT pathway. (2) m⁶A-modified E2F7 mRNA is stabilized by IGF2BP2, increasing E2F7 expression; E2F7, along with RUNX1 and CBFB, transcriptionally activates ITGA2, ITGA5, and NTRK1, activating the PI3K/AKT pathway. (3) The lncRNA ZFAS1, stabilized by m⁶A, acts as a molecular sponge for miR-100-3p, enhancing ATG10 expression and activating the PI3K/AKT pathway. (4) m⁶A-modified lncRNA FAM225A acts as a sponge for miR-590-3p and miR-1275, activating ITGB3 and subsequently the FAK/PI3K/AKT pathway. (5) In Taxol-resistant NPC cells, IGF2BP1 stabilizes m⁶A-modified AKT2 mRNA, increasing AKT2 expression. (6) In radioresistant NPC cells, YTHDC2 stabilizes m⁶A-modified IGF1R, enhancing AKT and S6 phosphorylation. (7) IGF2BP3 stabilizes m⁶A-modified NOTCH3 mRNA, activating Notch pathway. (8) ALYREF, recognizing NSUN2-mediated m⁵C-modified NOTCH1, stabilizes NOTCH1 mRNA, activating Notch signaling. B EMT: (1) m⁶A modification stabilizes TNKS mRNA, enhancing its expression, which promotes AXIN degradation via ubiquitination and activates β-catenin/TCF signaling. (2) The lncRNA ZFAS1, stabilized by m⁶A, acts as a molecular sponge for miR-100-3p, activating the PI3K/AKT pathway and promoting EMT. (3) m⁶A-modified Snail1 mRNA, recognized by IGF2BP2, is stabilized, increasing Snail1 expression. (4) KPNA2 mRNA, stabilized by IGF2BP3, is upregulated, promoting EMT. C Cancer Stemness: (1) IGF2BP3 stabilizes NOTCH3 mRNA in an m⁶A-dependent manner, activating the Notch pathway and promoting cancer stemness. (2) LINC00313, stabilized by m⁶A, recruits PTBP1, enhancing the STIM1/AKT axis and promoting cancer stemness. Green squares or upward arrows represent upregulated targets, while red squares or downward arrows indicate downregulated targets.

Fig. 4. Roles of RNA Modifications in Apoptosis, Ferroptosis, and Autophagy in NPC.

A Apoptosis: (1) m⁶A modification of ZNF750, recognized by IGF2BP3, facilitates ZNF750 degradation, disrupting the FGF14 axis, inhibiting apoptosis, and supporting NPC growth. (2) HNRNPK suppresses apoptosis in NPC cells by activating FLIP transcriptionally. (3) In the cytoplasm, HNRNPK stabilizes TP, blocking apoptosis in tumor cells. B Ferroptosis: (1) In radioresistant NPC cells, FTO upregulation removes m⁶A from OTUB1 transcripts, stabilizing OTUB1 and allowing it to recruit SLC7A11, which inhibits radiation-induced ferroptosis, promoting tumorigenesis. (2) NAT10 enhances sorafenib resistance by upregulating SLC7A11 expression through ac4C acetylation. (3) FTO-mediated demethylation of CD44 transcripts reduces YTHDC1-mediated splicing, increasing CD44V levels, which inhibits irradiation-induced ferroptosis and contributes to radioresistance. C Autophagy: (1) ZFAS1, acting as a sponge for miR-100-3p, increases ATG10 expression, driving autophagy and supporting cancer progression. (2) LINC00313, stabilized by m⁶A recognition via IGF2BP1, interacts with PTBP1 to upregulate STIM1, activating the AKT/mTOR pathway, which suppresses autophagy and enhances cancer stemness. (3) m⁶A-modified TRIM11, stabilized by IGF2BP2, upregulates its expression, promoting Daple ubiquitination and p62-mediated selective autophagy. Reduced Daple levels lead to DVL upregulation, activating the β-catenin/ABCC9 axis and contributing to drug resistance. Green squares or upward arrows represent upregulated targets, while red squares or downward arrows indicate downregulated targets.

Fig. 5. Roles of RNA modifications in metabolism, immune invasion, and EBV infection in NPC.

A Metabolism: (1) METTL14-mediated m⁶A modifications on ANKRD22 mRNA, recognized by IGF2BP2, stabilize ANKRD22, enhancing its translation. ANKRD22 interacts with the citrate transporter SLC25A1, increasing intracellular acetyl-CoA levels to drive de novo lipid synthesis. (2) METTL14 stabilizes AOC1 mRNA via m⁶A modifications. AOC1 degrades polyamines, producing ROS as a byproduct. (3) LINC00839, stabilized by IGF2BP1, recruits TAF15 to activate AOC1 transcription. B Immune Invasion: Reduced levels of the m⁶A reader YTHDF3 in metastatic NPC impair CBX1 decay, resulting in elevated CBX1 levels. CBX1 upregulates PD-L1 via IFN-γ-STAT1 signaling, promoting immune evasion, and concurrently enhances cell proliferation by repressing MAP7 through H3K9me3-modified heterochromatin formation. C EBV Infection: (1) YTHDF1 destabilizes m⁶A-modified EBV transcripts, suppressing EBV infection and replication. (2) IFITM1 competes with EBV glycoproteins gH/gL and gB for EphA2 binding. YTHDF3, with DDX5, accelerates IFITM1 mRNA degradation via m⁶A, enhancing EphA2-mediated EBV infection. (3) During EBV infection, the immediate-early protein BZLF1 binds the METTL3 promoter, lowering METTL3 expression. This reduction decreases m⁶A modifications on KLF4 mRNA, preventing YTHDF2-mediated degradation, resulting in elevated KLF4 protein levels and promoting EBV infection in NPE cells. Green squares or upward arrows represent upregulated targets, while red squares or downward arrows indicate downregulated targets.